JAL-2189 format help

[jalview.git] / help / html / calculations / pca.html

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 071a2b5..c38d9ac 100755 (executable)
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -58,15 +58,15 @@
     pair of sequences - computed with one of the available score
     matrices, such as <a href="scorematrices.html#blosum62">BLOSUM62</a>,
     <a href="scorematrices.html#pam250">PAM250</a>, or the <a
-      href="scorematrices.html#simplenucleotide"
-    >simple single nucleotide substitution matrix</a>. The options
-    available for calculation are given in the <strong><em>Change
+      href="scorematrices.html#simplenucleotide">simple single
+      nucleotide substitution matrix</a>. The options available for
+    calculation are given in the <strong><em>Change
         Parameters</em></strong> menu.
   </p>
   <p>
-    <em>PCA Calculation modes</em><br /> The default Jalview calculation
-    mode (indicated when <em><strong>Jalview PCA
-        Calculation</strong></em> is ticked in the <strong><em>Change
+    <em>PCA Calculation modes</em><br /> The default Jalview
+    calculation mode (indicated when <em><strong>Jalview
+        PCA Calculation</strong></em> is ticked in the <strong><em>Change
         Parameters</em></strong> menu) is to perform a PCA on a matrix where elements
     in the upper diagonal give the sum of scores for mutating in one
     direction, and the lower diagonal is the sum of scores for mutating
@@ -74,10 +74,10 @@
     gives an asymmetric matrix, and a different PCA to a matrix produced
     with the method described in the paper by G. Casari, C. Sander and
     A. Valencia. Structural Biology volume 2, no. 2, February 1995 (<a
-      href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7749921"
-    >pubmed</a>) and implemented at the SeqSpace server at the EBI. This
-    method preconditions the matrix by multiplying it with its
-    transpose, and can be employed in the PCA viewer by unchecking the <strong><em>Jalview
+      href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7749921">pubmed</a>)
+    and implemented at the SeqSpace server at the EBI. This method
+    preconditions the matrix by multiplying it with its transpose, and
+    can be employed in the PCA viewer by unchecking the <strong><em>Jalview
         PCA Calculation</em></strong> option in the <strong><em>Change
         Parameters</em></strong> menu.
   </p>